What if? Mouse proteomics after gene inactivation

Gianazza, Elisabetta; Miller, Ingrid; Guerrini, Uliano; Palazzolo, Luca; Laurenzi, Tommaso; Parravicini, Chiara; Eberini, Ivano

doi:10.1016/j.jprot.2019.03.008

Cited by 3 publications

(1 citation statement)

References 288 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Hence, parallel to the various sequencing efforts, comprehensive studies at the proteome level have been performed in recent years and provided insight into the proteins that are differentially expressed between cells, tissues, organs, or organ systems, or are related to a specific condition or disease. These studies have revealed functional genomics insights beyond that derived from sequencing alone [17][18][19][20] . Such efforts have included the analysis of cells and tissues from wild type, transgenic, knockin, and knockout strains, and mice labeled in vivo with isotope using mass spectrometry-based methods [21][22][23][24] .…”

Section: Introductionmentioning

confidence: 99%

Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma

et al. 2021

View full text Add to dashboard Cite

We proteotyped blood plasma from 30 mouse knockout strains and corresponding wild-type mice from the International Mouse Phenotyping Consortium. We used targeted proteomics with internal standards to quantify 375 proteins in 218 samples. Our results provide insights into the manifested effects of each gene knockout at the plasma proteome level. We first investigated possible contamination by erythrocytes during sample preparation and labeled, in one case, up to 11 differential proteins as erythrocyte originated. Second, we showed that differences in baseline protein abundance between female and male mice were evident in all mice, emphasizing the necessity to include both sexes in basic research, target discovery, and preclinical effect and safety studies. Next, we identified the protein signature of each gene knockout and performed functional analyses for all knockout strains. Further, to demonstrate how proteome analysis identifies the effect of gene deficiency beyond traditional phenotyping tests, we provide in-depth analysis of two strains, C8a−/− and Npc2+/−. The proteins encoded by these genes are well-characterized providing good validation of our method in homozygous and heterozygous knockout mice. Ig alpha chain C region, a poorly characterized protein, was among the differentiating proteins in C8a−/−. In Npc2+/− mice, where histopathology and traditional tests failed to differentiate heterozygous from wild-type mice, our data showed significant difference in various lysosomal storage disease-related proteins. Our results demonstrate how to combine absolute quantitative proteomics with mouse gene knockout strategies to systematically study the effect of protein absence. The approach used here for blood plasma is applicable to all tissue protein extracts.

show abstract